/***************************************************************************
 *   Copyright (C) 2007 by Alexandre Masselot,,,   *
 *   alex@alex-laptop   *
 *                                                                         *
 *   This program is free software; you can redistribute it and/or modify  *
 *   it under the terms of the GNU Library General Public License as       *
 *   published by the Free Software Foundation; either version 2 of the    *
 *   License, or (at your option) any later version.                       *
 *                                                                         *
 *   This program is distributed in the hope that it will be useful,       *
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of        *
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
 *   GNU General Public License for more details.                          *
 *                                                                         *
 *   You should have received a copy of the GNU Library General Public     *
 *   License along with this program; if not, write to the                 *
 *   Free Software Foundation, Inc.,                                       *
 *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
 ***************************************************************************/
#include "utils/peaktheomsmsfactorybasic.h"
#include "utils/aminoacidinstancerbasic.h"
#include "utils/peptidemodifier.h"
#include "utils/peptidemsmsfactory.h"

#include <iostream>

using namespace std;
using namespace bol;

/**
 * 
 * @param argc 
 * @param argv 
 * @return 
 */
int main(int argc, char **argv){
  AminoAcidInstancerBasic aainstancer;
  aainstancer.setMasses();

  PeakTheoMsmsFactoryBasic peaktheofactory;
  peaktheofactory.setSeries("y,b",1);
  peaktheofactory.setSeries("y,b,y++",2);
  PeptideModifier peptmodifier;

  Peptide pept("PEPTIDE");
  peptmodifier.printPeptide(cout, &pept);
  cout<<endl;
  Spectrum<PeakTheoMsms*> theospectrum;
  peaktheofactory.computeTheoMasses(pept, theospectrum, 1, true);
  cout<<theospectrum<<endl<<endl;
  peaktheofactory.computeTheoMasses(pept, theospectrum, 2, true);
  cout<<theospectrum<<endl<<endl;
  peaktheofactory.computeTheoMasses(pept, theospectrum, 5, true);
  cout<<theospectrum<<endl<<endl;

  peptmodifier.addModif(new Modification("Cys_CAM C 57.02146"), false);
  PeptideMSMSFactory peptidemsmsfactory;
  peptidemsmsfactory.setPeptideModifier(&peptmodifier);

  Peptide pept2("PCTEDYLSLILNR");
  vector<Peptide> vpept;
  peptidemsmsfactory.createPeptides(pept2, vpept);
    for(vector<Peptide>::const_iterator it=vpept.begin(); it<vpept.end(); it++){
      peptmodifier.printPeptide(cout, &(*it));
      cout<<"\t"<<it->getMass();
      cout<<endl;
      theospectrum.clear();
      peaktheofactory.computeTheoMasses(*it, theospectrum, 2, true);
      cout<<theospectrum<<endl<<endl;
  }


}
